Base frequencies from DNA Sequences
base.freq computes the frequencies (absolute or relative) of
the four DNA bases (adenine, cytosine, guanine, and thymidine) from a
sample of sequences.
Ftab computes the contingency table with the absolute
frequencies of the DNA bases from a pair of sequences.
base.freq(x, freq = FALSE, all = FALSE) Ftab(x, y = NULL)
The base frequencies are computed over all sequences in the sample. All missing or unknown sites are discarded from the computations.
Ftab, if the argument
y is given then both
y are coerced as vectors and must be of equal length. If
y is not given,
x must be a matrix or a list and only
the two first sequences are used.
A numeric vector with names
c("a", "c", "g", "t"), or a four by
four matrix with similar dimnames.
data(woodmouse) base.freq(woodmouse) base.freq(woodmouse, TRUE) Ftab(woodmouse) Ftab(woodmouse[1, ], woodmouse[2, ]) # same than above Ftab(woodmouse[14:15, ]) # between the last two